I have just one normal sample and 3 tumors from the same patient. In this case is it ok to generate PoN using the following code?
gatk --java-options "-Xmx16g" Mutect2 \ -R $ref \ -I $BAMs/normal.bam \ -tumor normal \ --germline-resource somatic-hg38-af-only-gnomad.hg38.vcf \ -O $out/normal_for_pon.vcf.gz
Can I use the normal_for_pon.vcf.gz for subsequent steps?
I couldn't find much information about using just one normal sample in the tutorials. I'm using gatk v126.96.36.199.
Thanks for the help!